Matching Functions Legend:

Function 1: The simplest function, a constant times the length of the match.

Function 2: Square root of length of extended match times a constant.

Function 3: Log base 2 of length+1 of extended match times a constant.

Function 4: Relative entropy of substring composition with respect to background composition times length of extended match times a constant.

Function 5: Relative entropy of substring composition with respect to background composition times length of extended match times a constant. For length =1, normal match value prevents two identical sequences composed of only one letter from scoring zero if the background is the same letter.

Function 6: Shannon-Jensen entropy of substring composition versus the background composition times length of extended match times a constant.